Capstone Project - Whole-Genome Sequencing
This entry represents my Honors Capstone Thesis. The Johnson lab utilizes several transgenic strains of C. elegans in its investigation of the expression and effects of Hairy/Enhancer-of-Split proteins. The hlh-29::gfp strain was generated through insertion of an extrachromosomal concatemer into the Bristol N2 wild-type genome. My contribution to the Johnson lab was using whole-genome sequencing on the MinION Nanopore platform to identify the location of the concatemer and its structure.
We located the concatemer in Chromosome III, where it had deleted two putative transcripts with no phenotypic effect. Initial estimates placed the concatemer as being 250,000 bases (250 kb) long; our work revealed that it is at least 188 kb but may be as long as 2 million bases. We were unable to determine the structure of the entire insertion. Functional copies of the hlh-29::gfp transgene were identified. This study indicates that the hlh-29::gfp strain is an adequate animal model for future studies.
The final manuscript for this project is available through JMU Scholarly Commons. An abridged version is in preparation for microPublications Biology. This project was presented as a poster at the 2022 Honors Symposium and as a 15-minute talk at the 2022 Biotech Symposium.
The hlh-29::gfp and related strains are significant as animal models for basic science. The human homolog of hlh-29 has been implicated in both hormone-dependent (HDBC) and triple-negative breast cancers (TNBC). Observing how various treatments to the worms alter hlh-29 expression - as demonstrated by fluorescence of the GFP contained in the concatemer - could be the first step on the road to finding new targeted therapies for HDBC and TNBC. As a source of excess mortality for African American women versus non-Hispanic white women, harnessing biotechnological tools to target HDBC may be a way to alleviate a known health disparity.
We located the concatemer in Chromosome III, where it had deleted two putative transcripts with no phenotypic effect. Initial estimates placed the concatemer as being 250,000 bases (250 kb) long; our work revealed that it is at least 188 kb but may be as long as 2 million bases. We were unable to determine the structure of the entire insertion. Functional copies of the hlh-29::gfp transgene were identified. This study indicates that the hlh-29::gfp strain is an adequate animal model for future studies.
The final manuscript for this project is available through JMU Scholarly Commons. An abridged version is in preparation for microPublications Biology. This project was presented as a poster at the 2022 Honors Symposium and as a 15-minute talk at the 2022 Biotech Symposium.
The hlh-29::gfp and related strains are significant as animal models for basic science. The human homolog of hlh-29 has been implicated in both hormone-dependent (HDBC) and triple-negative breast cancers (TNBC). Observing how various treatments to the worms alter hlh-29 expression - as demonstrated by fluorescence of the GFP contained in the concatemer - could be the first step on the road to finding new targeted therapies for HDBC and TNBC. As a source of excess mortality for African American women versus non-Hispanic white women, harnessing biotechnological tools to target HDBC may be a way to alleviate a known health disparity.
